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http://www.utsouthwestern.edu/education/medical-school/departments/neurology/programs/traumatic-brain-injury/index.html

The 16 affiliated Model System centers throughout the United States are responsible for gathering and submitting the core data set to the national database as well as conducting research studies on traumatic brain injury (TBI) both in collaboration with the other centers and within our own site. Through our research we hope to learn more about TBI and about the issues and concerns of people with TBI. Our goals are to improve the outcome and quality of life for people who have had brain injuries and for those who are caring for the person with a TBI. The North Texas Traumatic Brain Injury Model System (NT-TBIMS) pools the efforts and talents of individuals from the Departments of Neurosurgery, Neurology, Physical Medicine and Rehabilitation, Psychiatry (Neuropsychiatry), and Neuroradiology of the two leading medical institutions in the North Texas region. To be a patient involved in the research being conducted by the North Texas Traumatic Brain Injury Model System you must have suffered a TBI, be at least 16 years of age, have received initial treatment for the TBI at either Parkland Health and Hospital System or Baylor University Medical Center and then have received rehabilitative care at either Parkland, University Hospital Zale-Lipshy, or Baylor Institute for Rehabilitation. The patient must also be able to understand and sign an informed consent to participate or, if unable, have a family member or a legal guardian who understands the form sign the informed consent for the patient.

Proper citation: North Texas Traumatic Brain Injury Model System (RRID:SCR_005879) Copy   

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http://brainnetworks.sourceforge.net

Brain Networks: Code to perform network analysis on brain imaging data.

Proper citation: Brain Networks (RRID:SCR_005841) Copy   

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http://www.fmriconsulting.com/brodmann/

An atlas that facilitates fMRI analysis understanding by providing access to all of the functions that have been associated with each of the 52 Brodmann's areas or corresponding gyri. Links to main publications supporting the findings are provided in PubMed ID format. Brodmann's areas with similar functions and locations have been collapsed into a single page. The word left or right has been added indicating a lateralized function. All the abstracts published on PubMed on fMRI and brain PET studies in which the Brodmann's area or its anatomical correlate were mentioned have been reviewed up to August 2008. Abstracts with poorly described experimental methods or findings clearly conflicting with established knowledge provided by the clinical model were excluded. Studies on patients were also excluded.

Proper citation: Brodmann's Interactive Atlas (RRID:SCR_006368) Copy   

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http://www.zebrafinch.org/

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 29, 2016. Project to advance understanding of the neural mechanisms of vocal learning by providing a quantitative description of the relationship between physiological variables and vocal performance over the course of development in a songbird, the zebra finch. They propose to study vocal learning dynamically across neuronal and peripheral subsystems, using a novel collaborative approach that will harness the combined expertise of several investigators. Their proposed research model will 1) provide simultaneous measurements of acoustic, articulatory and electrophysiological data that will document the detailed dynamics of the vocal imitation process in a standardized learning paradigm; and 2) incorporate these measurements into a theoretical/computational framework that simultaneously provides a phenomenological description and attempts to elucidate the mechanistic basis of the learning process.

Proper citation: Zebra Finch Song Learning Consortium (RRID:SCR_006356) Copy   

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http://www.parkinsons.org.uk/content/parkinsons-uk-brain-bank

A brain bank of the United Kingdom which collects human brains for Parkinsons disease research. The collection is comprised of brain, spinal cord and a sample of cerebrospinal fluid from people with and without Parkinson's after death. Researchers can fill out a brain tissue request form to order samples from the bank.

Proper citation: Parkinsons UK Brain Bank (RRID:SCR_007030) Copy   

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http://www.nervenet.org/main/dictionary.html

A mouse-related portal of genomic databases and tables of mouse brain data. Most files are intended for you to download and use on your own personal computer. Most files are available in generic text format or as FileMaker Pro databases. The server provides data extracted and compiled from: The 2000-2001 Mouse Chromosome Committee Reports, Release 15 of the MIT microsatellite map (Oct 1997), The recombinant inbred strain database of R.W. Elliott (1997) and R. W. Williams (2001), and the Map Manager and text format chromosome maps (Apr 2001). * LXS genotype (Excel file): Updated, revised positions for 330 markers genotyped using a panel of 77 LXS strain. * MIT SNP DATABASE ONLINE: Search and sort the MIT Single Nucleotide Polymorphism (SNP) database ONLINE. These data from the MIT-Whitehead SNP release of December 1999. * INTEGRATED MIT-ROCHE SNP DATABASE in EXCEL and TEXT FORMATS (1-3 MB): Original MIT SNPs merged with the new Roche SNPs. The Excel file has been formatted to illustrate SNP haplotypes and genetic contrasts. Both files are intended for statistical analyses of SNPs and can be used to test a method outlined in a paper by Andrew Grupe, Gary Peltz, and colleagues (Science 291: 1915-1918, 2001). The Excel file includes many useful equations and formatting that will help in navigating through this large database and in testing the in silico mapping method. * Use of inbred strains for the study of individual differences in pain related phenotypes in the mouse: Elissa J. Chesler''s 2002 dissertation, discussing issues relevant to the integration of genomic and phenomic data from standard inbred strains including genetic interactions with laboratory environmental conditions and the use of various in silico inbred strain haplotype based mapping algorithms for QTL analysis. * SNP QTL MAPPER in EXCEL format (572 KB, updated January 2002 by Elissa Chesler): This Excel workbook implements the Grupe et al. mapping method and outputs correlation plots. The main spreadsheet allows you to enter your own strain data and compares them to haplotypes. Be very cautious and skeptical when using this spreadsheet and the technique. Read all of the caveates. This excel version of the method was developed by Elissa Chesler. This updated version (Jan 2002) handles missing data. * MIT SNP Database (tab-delimited text format): This file is suitable for manipulation in statistics and spreadsheet programs (752 KB, Updated June 27, 2001). Data have been formatted in a way that allows rapid acquisition of the new data from the Roche Bioscience SNP database. * MIT SNP Database (FileMaker 5 Version): This is a reformatted version of the MIT Single Nucleotide Polymorphism (SNP) database in FileMaker 5 format. You will need a copy of this application to open the file (Mac and Windows; 992 KB. Updated July 13, 2001 by RW). * Gene Mapping and Map Manager Data Sets: Genetic maps of mouse chromosomes. Now includes a 10th generation advanced intercross consisting of 500 animals genetoyped at 340 markers. Lots of older files on recombinant inbred strains. * The Portable Dictionary of the Mouse Genome, 21,039 loci, 17,912,832 bytes. Includes all 1997-98 Chromosome Committee Reports and MIT Release 15. * FullDict.FMP.sit: The Portable Dictionary of the Mouse Genome. This large FileMaker Pro 3.0/4.0 database has been compressed with StuffIt. The Dictionary of the Mouse Genome contains data from the 1997-98 chromosome committee reports and MIT Whitehead SSLP databases (Release 15). The Dictionary contains information for 21,039 loci. File size = 4846 KB. Updated March 19, 1998. * MIT Microsatellite Database ONLINE: A database of MIT microsatellite loci in the mouse. Use this FileMaker Pro database with OurPrimersDB. MITDB is a subset of the Portable Dictionary of the Mouse Genome. ONLINE. Updated July 12, 2001. * MIT Microsatellite Database: A database of MIT microsatellite loci in the mouse. Use this FileMaker Pro database with OurPrimersDB. MITDB is a subset of the Portable Dictionary of the Mouse Genome. File size = 3.0 MB. Updated March 19, 1998. * OurPrimersDB: A small database of primers. Download this database if you are using numerous MIT primers to map genes in mice. This database should be used in combination with the MITDB as one part of a relational database. File size = 149 KB. Updated March 19, 1998. * Empty copy (clone) of the Portable Dictionary in FileMaker Pro 3.0 format. Download this file and import individual chromosome text files from the table into the database. File size = 231 KB. Updated March 19, 1998. * Chromosome Text Files from the Dictionary: The table lists data on gene loci for individual chromosomes.

Proper citation: Mouse Genome Databases (RRID:SCR_007147) Copy   

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http://med.stanford.edu/narcolepsy.html

The Stanford Center for Narcolepsy was established in the 1980s as part of the Department of Psychiatry and Behavioral Sciences. Today, it is the world leader in narcolepsy research with more than 100 articles on narcolepsy to its name. The Stanford Center for Narcolepsy was the first to report that narcolepsy-cataplexy is caused by hypocretin (orexin) abnormalities in both animal models and humans. Under the direction of Drs. Emmanuel Mignot and Seiji Nishino, the Stanford Center for Narcolepsy today treats several hundred patients with the disorder each year, many of whom participate in various research protocols. Other research protocols are conducted in animal models of narcolespy. We are always looking for volunteers in our narcolepsy research studies. We are presently recruiting narcoleptic patients for genetic studies, drug clinical trials, hypocretin measurement studies in the CSF and functional MRI studies. Monetary gifts to the Center for Narcolepsy are welcome. If you wish to make the ultimate gift, please consider participating in our Brain Donation Program. To advance our understanding of the cause, course, and treatment of narcolepsy, in 2001 Stanford University started a program to obtain human brain tissue for use in narcolepsy research. Donated brains provide an invaluable resource and we have already used previously donated brains to demonstrate that narcolepsy is caused by a lack of a very specific type of cell in the brain, the hypocretin (orexin) neuron. While the brain donations do not directly help the donor, they provide an invaluable resource and a gift to others. The real answers as to what causes or occurrs in the brain when one has narcolepsy will only be definitively understood through the study of brain tissue. Through these precious donations, narcolepsy may eventually be prevented or reversible. We currently are seeking brains from people with narcolepsy (with cataplexy and without), idiopathic hypersomnia and controls or people without a diagnosed sleep disorder of excessive sleepiness. Control brains are quite important to research, as findings must always be compared to tissue of a non-affected person. Friends and loved ones of people who suffer with narcoleps may wish to donate to our program to help fill this very important need. Refer to the Movies tab for movies of Narcolepsy / Cataplexy.

Proper citation: Stanford Center for Narcolepsy (RRID:SCR_007021) Copy   

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http://www.bmu.psychiatry.cam.ac.uk/software/

Suite of programs developed for fMRI analysis in a Virtual Pipeline Laboratory facilitates combining program modules from different software packages into processing pipelines to create analysis solutions which are not possible with a single software package alone. Current pipelines include fMRI analysis, statistical testing based on randomization methods and fractal spectral analysis. Pipelines are continually being added. The software is mostly written in C. This fMRI analysis package supports batch processing and comprises the following general functions at the first level of individual image analysis: movement correction (interpolation and regression), time series modeling, data resampling in the wavelet domain, hypothesis testing at voxel and cluster levels. Additionally, there is code for second level analysis - group and factorial or ANOVA mapping - after co-registration of voxel statistic maps from individual images in a standard space. The main point of difference from other fMRI analysis packages is the emphasis throughout on the use of data resampling (permutation or randomization) as a basis for inference on individual, group and factorial test statistics at voxel and cluster levels of resolution.

Proper citation: Cambridge Brain Activation (RRID:SCR_007109) Copy   

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http://openccdb-dev-web.crbs.ucsd.edu/software/index.shtm

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on May 4th,2023. Software to support registering brain images to the stereotaxic coordinate system of a brain atlas. It was specifically designed to work with the large scale brain mosaics. When data are uploaded to the CCDB, users may launch Jibber, a custom tool for defining correspondence points between the image and an atlas overlay. Jibber automatically downsamples the data, so that users can define the warping and scaling parameters with good interactive performance on the smaller copy. Once the warping transformation is computed, the original image and the transformation matrix are sent to a cluster of computers for warping. The current version of Jetsam is running on a 30 Sun V20 nodes and the execution time is roughly about 20 minutes per GB. The warped images are then automatically registered with an image web server that supports spatial queries based on stereotaxic coordinates. These servers generate optimized downsampled images, which can be displayed by standard online clients regardless of the size of the original image.

Proper citation: Image Workflow (RRID:SCR_007017) Copy   

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https://www.nitrc.org/projects/fmridatacenter/

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 25, 2013 Public curated repository of peer reviewed fMRI studies and their underlying data. This Web-accessible database has data mining capabilities and the means to deliver requested data to the user (via Web, CD, or digital tape). Datasets available: 107 NOTE: The fMRIDC is down temporarily while it moves to a new home at UCLA. Check back again in late Jan 2013! The goal of the Center is to help speed the progress and the understanding of cognitive processes and the neural substrates that underlie them by: * Providing a publicly accessible repository of peer-reviewed fMRI studies. * Providing all data necessary to interpret, analyze, and replicate these fMRI studies. * Provide training for both the academic and professional communities. The Center will accept data from those researchers who are publishing fMRI imaging articles in peer-reviewed journals. The goal is to serve the entire fMRI community.

Proper citation: fMRI Data Center (RRID:SCR_007278) Copy   

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http://www.nia.nih.gov/research/dab/aged-rodent-tissue-bank-handbook/tissue-arrays

Offer high-throughput analysis of tissue histology and protein expression for the biogerontology research community. Each array is a 4 micron section that includes tissue cores from multiple tissues at multiple ages on one slide. The arrays are made from ethanol-fixed tissue and can be used for all techniques for which conventional tissue sections can be used. Ages are chosen to span the life from young adult to very old age. (available ages: 4, 12, 18, 24 and 28 months of age) Images of H&E stained punches are available for Liver, Cardiac Muscle, and Brain. The NIA aged rodent tissue arrays were developed with assistance from the National Cancer Institute (NCI) Tissue Array Research Program (TARP), led by Dr. Stephen Hewitt, Director. NCI TARP contains more information on tissue array construction, protocols for using arrays, and references. Preparation and Product Description Tissue arrays are prepared in parallel from different sets of animals so that experiments can be conducted in duplicate, with each array using unique animals with a unique product number. The product descriptions page describes each array, including: * Strain * Gender * Ages * Tissues * Animal Identification Numbers

Proper citation: Aged Rodent Tissue Arrays (RRID:SCR_007332) Copy   

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https://ida.loni.usc.edu/login.jsp

Archive used for archiving, searching, sharing, tracking and disseminating neuroimaging and related clinical data. IDA is utilized for dozens of neuroimaging research projects across North America and Europe and accommodates MRI, PET, MRA, DTI and other imaging modalities.

Proper citation: LONI Image and Data Archive (RRID:SCR_007283) Copy   

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http://human.brain-map.org/static/brainexplorer

Multi modal atlas of human brain that integrates anatomic and genomic information, coupled with suite of visualization and mining tools to create open public resource for brain researchers and other scientists. Data include magnetic resonance imaging (MRI), diffusion tensor imaging (DTI), histology and gene expression data derived from both microarray and in situ hybridization (ISH) approaches. Brain Explorer 2 is desktop software application for viewing human brain anatomy and gene expression data in 3D.

Proper citation: Allen Human Brain Atlas (RRID:SCR_007416) Copy   

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http://www.neurolens.org/NeuroLens/

An integrated environment for the analysis and visualization of functional neuroimages. It is intended to provide extremely fast and flexible image processing, via an intuitive user interface that encourages experimentation with analysis parameters and detailed inspection of both raw image data and processing results. All processing operations in NeuroLens are built around a Plugin architecture, making it easy to extend its functionality. NeuroLens runs on Apple computers based on the G4, G5, or Intel chipsets and running MacOSX 10.4 (Tiger) or later. It is available free for academic and non-profit research use. * Operating System: MacOS * Programming Language: Objective C * Supported Data Format: AFNI BRIK, ANALYZE, COR, DICOM, MGH/MGZ, MINC, Other Format

Proper citation: NeuroLens (RRID:SCR_007372) Copy   

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http://enhancer.lbl.gov/

Resource for experimentally validated human and mouse noncoding fragments with gene enhancer activity as assessed in transgenic mice. Most of these noncoding elements were selected for testing based on their extreme conservation in other vertebrates or epigenomic evidence (ChIP-Seq) of putative enhancer marks. Central public database of experimentally validated human and mouse noncoding fragments with gene enhancer activity as assessed in transgenic mice. Users can retrieve elements near single genes of interest, search for enhancers that target reporter gene expression to particular tissue, or download entire collections of enhancers with defined tissue specificity or conservation depth.

Proper citation: VISTA Enhancer Browser (RRID:SCR_007973) Copy   

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https://med.uth.edu/nrc/

The Neuroscience Research Center (NRC) is a university-wide center where diverse and multidisciplinary research is conducted to further the understanding of neural and behavioral disorders. Whether conducting cellular research in laboratories or clinical trials in patient care settings, the work of NRC researchers may someday contribute to preventing and treating such devastating disorders as: * Dementias resulting from Alzheimer''s disease and stroke * Mental retardation and other learning disabilities * Mental illnesses, including schizophrenia and manic-depressive illness * Alcoholism and other substance abuse problems * Inability to process knowledge due to factors such as aging and head trauma * Disabilities due to disorders of the developing nervous system More than 280 faculty hold NRC appointments, and are on the faculties of the Medical School, School of Public Health, School of Nursing, Dental Branch, and School of Biomedical Informatics. Departments with significant NRC research activities within the Medical School include Neurobiology and Anatomy; Neurology; Neurosurgery; Ophthalmology and Visual Science; Psychiatry and Behavioral Sciences and Radiology. NRC activities are guided by an executive committee appointed by the President of the Health Science Center. The Neuroscience Research Center (NRC) is affiliated with educational opportunities at the graduate and postdoctoral levels.

Proper citation: UTHealth at Houston Neuroscience Research Center (RRID:SCR_007486) Copy   

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http://www.nibb.ac.jp/brish/indexE.html

Database of detailed protocols for single and double in situ hybridization (ISH) method, probes used by Yamamori lab and others useful for studies of brain, and many photos of mammalian (mostly mouse and monkey) brains stained with various gene probes. Also includes a brain atlas of gene expression. Currently, the atlas comprises a series of un-annotated images showing the localization of a particular probe or molecule, e.g., AChE.

Proper citation: BraInSitu: A homepage for molecular neuroanatomy (RRID:SCR_008081) Copy   

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http://sig.biostr.washington.edu/projects/brain/

The UW Integrated Brain Project is one project within the national Human Brain Project, a national multi-agency effort to develop informatics tools for managing the exploding amount of information that is accumulating about the human brain. The objective of the UW Integrated Brain Project effort is to organize and integrate distributed functional information about the brain around the structural information framework that is the long term goal of our work. This application therefore extends the utility of the Digital Anatomist Project by using it to organize non-structural information. The initial driving neuroscience problem that is being addressed is the management, visualization and analysis of cortical language mapping data. In recent years, advances in imaging technology such as PET and functional MRI have allowed researchers to observe areas of the cortex that are activated when the subject performs language tasks. These advances have greatly accelerated the amount of data available about human language, but have also emphasized the need to organize and integrate the sometimes contradictory sources of data, in order to develop theories about language organization. The hypothesis is that neuroanatomy is the common substrate on which the diverse kinds of data can be integrated. A result of the work done by this project is a set of software tools for generating a 3-D reconstruction of the patient''s own brain from MRI, for mapping functional data to this reconstruction, for normalizing individual anatomy by warping to a canonical brain atlas and by annotating data with terms from an anatomy ontology, for managing individual lab data in local laboratory information systems, for integrating and querying data across separate data management systems, and for visualizing the integrated results. Sponsors: This Human Brain Project research is funded jointly by the National Institute on Deafness and Other Communication Disorders, the National Institute of Mental Health, and the National Institute on Aging.

Proper citation: University of Washington Integrated Brain Project (RRID:SCR_008075) Copy   

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http://mmil.ucsd.edu/

An interdisciplinary group of scientists and clinicians who study the human brain using a variety of imaging, recording, and computational techniques. Their primary goal is to bridge non-invasive imaging technologies to the underlying neurophysiology of brain neuronal circuits for a better understanding of healthy human brain function, and mechanisms of disruption of this function in diseases such as Alzheimer's, epilepsy and stroke. The other goal of the MMIL is to develop and apply advanced imaging techniques to understanding the human brain and its disorders. In order to ground these methodological developments in their underlying neurobiology, invasive studies in humans and animals involving optical and micro physiological measures are also performed. These methodologies are applied to understanding normal function in sleep, memory and language, development and aging, and diseases such as dementia, epilepsy and autism.

Proper citation: Multimodal Imaging Laboratory (RRID:SCR_008071) Copy   

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http://www.cabiatl.com/mricro/

MRIcro allows Windows and Linux computers view medical images. It is a standalone program, but includes tools to complement SPM (software that allows neuroimagers to analyze MRI, fMRI and PET images). MRIcro allows efficient viewing and exporting of brain images. In addition, it allows neuropsychologists to identify regions of interest (ROIs, e.g. lesions). MRIcro can create Analyze format headers for exporting brain images to other platforms. Some features of MRIcro are: - Converts medical images to SPM friendly Analyze format. - View Analyze format images (big or little endian). - Create Analyze format headers (big or little endian). - Create 3D regions of interest (with computed volume & intensity). - Overlap multiple regions of interest. - Rotate images to match SPM template images. - Export images to BMP, JPEG, PNG or TIF format. - Yoked images: linked viewing of multiple images (e.g. view same coordinates of PET and MRI scans). Users familiar with other Windows programs will find that this software is fairly straightforward to use. Resting the mouse cursor over a button will cause a text hint to appear over the button. However, a tutorial with a step by step guide of how to use MRIcro with SPM is available.

Proper citation: MRIcro Software (RRID:SCR_008264) Copy   

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